CEL p.Ala601Pro
c.1801G>C · rs756704908 · VCV1194884
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.74%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.212 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.18 | GERP -1.4 |
| Regional constraint | o/e 1.11 | unconstrained · MANE · 642 bp · p 0.096 · regional, not allelic |
| Overall | ||
| CADD | 17.67 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.74%
South Asian · 1,286/46,926 alleles
Filtering AF
2.62%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.57%
Overall
0.73%
3,794/519,998 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 2.74% | 36 |
| Middle Eastern | 2.05% | 49 |
| Ashkenazi Jewishnot grpmax-eligible | 1.62% | 62 |
| Remaining individualsnot grpmax-eligible | 0.702% | 143 |
| Finnishnot grpmax-eligible | 0.651% | 154 |
| European (non-Finnish) | 0.541% | 185 |
| Admixed American | 0.411% | 243 |
| Amishnot grpmax-eligible | 0.342% | 292 |
| East Asian | 0.079% | 1,266 |
| African / African-American | 0.0761% | 1,314 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- CEL
- Protein
- p.Ala601Pro
- Coding
- c.1801G>C
- MANE Select
- NM_001807
- dbSNP
- rs756704908
- Type
- single nucleotide variant
- Location
- chr9:133071303 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.10 · 7 PDB
- Residue 601
- the 'disordered' region; the '17 x 11 aa tandem repeats, glycodomain, o-linked (mucin type)' region
Similar variants
- CEL p.Ala601Gly Uncertain significance ★ same residue
- CEL p.Ala601Asp Likely benign ★ same residue
- CEL p.Ala601Thr Benign ★ same residue
- CEL p.Ala601fs Conflicting classifications of pathogenicity ★ same residue
- CEL c.67-3C>A Uncertain significance ★★ same type
- CEL p.Ala295Ser Uncertain significance ★★ same type
- CEL p.Ala548Glu Uncertain significance ★★ same type
- CEL p.Ala722Val Uncertain significance ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cel-p-ala601pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown